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Merge branch 'main' into translate-propogation

tlambert03:translate-propogation

2 days ago

fix: assign fov names for plate positions with grid_plan (#136) * fix: assign fov names for plate positions in _build_stage_positions_plan When stage_positions have plate_row/plate_col but no explicit name, generate fov-indexed names consistent with WellPlatePlan: - With grid: fov0, fov1, ... per grid point within each well - Without grid: fov0 (single FOV per well) - Explicit names are always preserved Closes #131 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * refactor: move all naming logic out of _pos_with_grid_point Extract _grid_position_name helper that centralizes all position naming: - Explicit user name (with RandomPoints suffix when needed) - fov{index} for plate positions - str(position_index) fallback _pos_with_grid_point now only handles coordinate merging. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * refactor: remove has_plate parameter from _grid_position_name _grid_position_name now checks pos.plate_row/plate_col directly instead of taking a pre-computed has_plate flag. Same for the no-grid branch in _build_stage_positions_plan. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * style: clean up grid-first loop and shared positions declaration Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> * refactor: unify naming through _grid_position_name for all positions Use _grid_position_name for both grid-expanded and standalone positions, eliminating duplicated naming logic. Update docstring with full parameter docs and examples. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

main

2 days ago

feat: add `set_global_metadata()` method (#133) * wip * refactor: remove unused get_metadata method from ScratchBackend * feat: enhance summary metadata handling for OME-TIFF backend to support multiple positions * remove comment * feat: persist summary metadata to manifest.json in disk-backed mode * feat: add thread safety to summary metadata handling in TIFF backend * rename to global metadata * rename file * refactor: rename summary_metadata to global_metadata in ScratchBackend and update related tests * refactor: rename summary_metadata to global_metadata in AcquireZarrBackend, ScratchBackend, and TiffBackend * refactor: update metadata handling in OMEStream and TiffBackend for improved structure * refactor: update test to use global_metadata instead of summary_metadata in manifest * refactor: streamline imports and remove unnecessary skips in test_global_metadata * pin ty * refactor: remove unused JsonDocumentMirror test and related imports * refactor: simplify dirty state management in AcquireZarrBackend and YaozarrsBackend * refactor: support post-finalize tiff metadata * refactor: enhance global metadata handling in AcquireZarrBackend and add tests for single-position layouts * refactor: update metadata preparation notes and clean up unused imports in TiffBackend * refactor: implement set_map_annotation method in OmeXMLMirror and update TiffBackend to use it * refactor: streamline AcquisitionSettings usage in global metadata tests

main

4 days ago

feat: add stage label generation from position coordinates in OME-TIFF

tlambert03:translate-propogation

8 days ago

feat: add `set_global_metadata()` method (#133) * wip * refactor: remove unused get_metadata method from ScratchBackend * feat: enhance summary metadata handling for OME-TIFF backend to support multiple positions * remove comment * feat: persist summary metadata to manifest.json in disk-backed mode * feat: add thread safety to summary metadata handling in TIFF backend * rename to global metadata * rename file * refactor: rename summary_metadata to global_metadata in ScratchBackend and update related tests * refactor: rename summary_metadata to global_metadata in AcquireZarrBackend, ScratchBackend, and TiffBackend * refactor: update metadata handling in OMEStream and TiffBackend for improved structure * refactor: update test to use global_metadata instead of summary_metadata in manifest * refactor: streamline imports and remove unnecessary skips in test_global_metadata * pin ty * refactor: remove unused JsonDocumentMirror test and related imports * refactor: simplify dirty state management in AcquireZarrBackend and YaozarrsBackend * refactor: support post-finalize tiff metadata * refactor: enhance global metadata handling in AcquireZarrBackend and add tests for single-position layouts * refactor: update metadata preparation notes and clean up unused imports in TiffBackend * refactor: implement set_map_annotation method in OmeXMLMirror and update TiffBackend to use it * refactor: streamline AcquisitionSettings usage in global metadata tests

main

9 days ago

feat: add `set_global_metadata()` method (#133) * wip * refactor: remove unused get_metadata method from ScratchBackend * feat: enhance summary metadata handling for OME-TIFF backend to support multiple positions * remove comment * feat: persist summary metadata to manifest.json in disk-backed mode * feat: add thread safety to summary metadata handling in TIFF backend * rename to global metadata * rename file * refactor: rename summary_metadata to global_metadata in ScratchBackend and update related tests * refactor: rename summary_metadata to global_metadata in AcquireZarrBackend, ScratchBackend, and TiffBackend * refactor: update metadata handling in OMEStream and TiffBackend for improved structure * refactor: update test to use global_metadata instead of summary_metadata in manifest * refactor: streamline imports and remove unnecessary skips in test_global_metadata * pin ty * refactor: remove unused JsonDocumentMirror test and related imports * refactor: simplify dirty state management in AcquireZarrBackend and YaozarrsBackend * refactor: support post-finalize tiff metadata * refactor: enhance global metadata handling in AcquireZarrBackend and add tests for single-position layouts * refactor: update metadata preparation notes and clean up unused imports in TiffBackend * refactor: implement set_map_annotation method in OmeXMLMirror and update TiffBackend to use it * refactor: streamline AcquisitionSettings usage in global metadata tests

main

9 days ago

refactor: streamline AcquisitionSettings usage in global metadata tests

tlambert03:summary-meta

9 days ago

refactor: implement set_map_annotation method in OmeXMLMirror and update TiffBackend to use it

tlambert03:summary-meta

9 days ago

Latest Branches

+61%

fix: Ensure position coordinates are propagated to zarr coordinateTransforms and OME StageLabel#134

2 days ago

37d3e76

tlambert03:translate-propogation

-40%

feat: add `set_global_metadata()` method#133

9 days ago

3a0f19d

tlambert03:summary-meta

+2%

feat: support plate metadata from position annotations (useq-schema >=0.9.2)#130

20 days ago

15d9612

tlambert03:use-new-useq

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